Variant report

Variant	rs4489092
Chromosome Location	chr5:90420644-90420645
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90418737..90421157-chr5:90426368..90428230,2	K562	blood:
2	chr5:90413771..90418676-chr5:90419460..90425678,7	K562	blood:
3	chr5:90419738..90423314-chr5:90675814..90678052,4	K562	blood:
4	chr5:90419568..90422226-chr5:90422771..90425466,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10063704	0.89[CEU][hapmap]
rs10454910	0.92[YRI][hapmap]
rs10942625	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11739054	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12188249	0.86[YRI][hapmap]
rs12518689	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12657388	0.80[AFR][1000 genomes]
rs13154380	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1808084	0.89[CEU][hapmap]
rs1852732	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2367280	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2367282	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2367283	0.88[CEU][hapmap]
rs4386756	0.87[YRI][hapmap];0.80[AFR][1000 genomes]
rs4512153	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4608951	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4916845	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7707023	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7731652	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90396200-90422800	Weak transcription	Esophagus	oesophagus
2	chr5:90401600-90431800	Weak transcription	K562	blood
3	chr5:90403000-90431600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:90403200-90431600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:90406600-90421800	Weak transcription	Small Intestine	intestine
6	chr5:90411000-90421600	Weak transcription	Brain Hippocampus Middle	brain
7	chr5:90415000-90421800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr5:90415400-90422600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:90415600-90422000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:90416000-90420800	Weak transcription	Left Ventricle	heart
11	chr5:90416000-90420800	Weak transcription	Pancreas	Pancrea
12	chr5:90416000-90422200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr5:90416000-90422600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:90416000-90422600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr5:90416000-90430000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:90416200-90421600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr5:90416200-90421800	Weak transcription	Stomach Mucosa	stomach
18	chr5:90416600-90421600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr5:90416600-90421800	Weak transcription	Fetal Stomach	stomach
20	chr5:90416600-90422200	Weak transcription	Fetal Muscle Leg	muscle
21	chr5:90416600-90422600	Weak transcription	Lung	lung
22	chr5:90416800-90421000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:90418000-90422200	Weak transcription	HMEC	breast
24	chr5:90418400-90421800	Weak transcription	Fetal Brain Male	brain
25	chr5:90418600-90435600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr5:90418800-90421400	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr5:90418800-90421600	Weak transcription	Fetal Lung	lung
28	chr5:90418800-90422000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr5:90419000-90421000	Weak transcription	Fetal Brain Female	brain
30	chr5:90419000-90423200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr5:90419200-90424000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr5:90419400-90420800	Weak transcription	Psoas Muscle	Psoas
33	chr5:90419400-90420800	Weak transcription	Right Atrium	heart
34	chr5:90419400-90421600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr5:90419400-90422200	Weak transcription	Placenta	Placenta
36	chr5:90419600-90421000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr5:90419600-90421200	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr5:90419600-90425000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr5:90419800-90420800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr5:90419800-90421000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr5:90419800-90421200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr5:90419800-90421200	Weak transcription	Brain Anterior Caudate	brain
43	chr5:90419800-90421800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr5:90419800-90422400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr5:90419800-90431400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr5:90420000-90420800	Weak transcription	Ovary	ovary
47	chr5:90420000-90421800	Weak transcription	NHDF-Ad	bronchial
48	chr5:90420000-90422200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr5:90420000-90422600	Weak transcription	Aorta	Aorta
50	chr5:90420400-90421400	Weak transcription	NHLF	lung

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